Package gov.nih.mipav.model.algorithms

Class AlgorithmPbBoundaryDetection

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmPbBoundaryDetection

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmPbBoundaryDetection
extends AlgorithmBase

Compute probability of boundary using brightness gradient and texture gradient Original MATLAB code written by David R. Martin in April 2003 Reference: "Learning to Detect Natural Image Boundaries Using Local Brightness, Color, and Texture Cues" by David R. Martin, Charles C. Fowlkes, and Jitendra Malik, IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 26, No. 5, May, 2004, pp. 530-549.

Author:

ilb

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	BG
private static final int	BGTG
private final byte[]	byteIntBuffer	byte array for int *
private final byte[]	byteLongBuffer	byte array for long *
private final byte[]	byteShortBuffer	byte array for short *
private static final int	CANNY
private static final int	CG
private static final int	CGTG
private static final int	COLOR_PRESENTATION
private final double	epsilon
private static final int	GM
private static final int	GM2
private int	gradientType
private static final int	GRAY_PRESENTATION
private double	highRadius
private double	hmult
private double	lowRadius
private int	nthresh
private int	numOrientations
private int	presentation
private RandomAccessFile	raFile
private double	sigma
private String	smooth
private static final int	TG
private static final int	TWOMM
private static final int	TWOMM2
private int	xDim
private int	yDim

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmPbBoundaryDetection()	AlgorithmPbBoundaryDetection - default constructor.
AlgorithmPbBoundaryDetection(ModelImage destImg, ModelImage srcImg, int gradientType, int presentation, double lowRadius, double highRadius, int numOrientations, String smooth, double sigma, int nthresh, double hmult)	AlgorithmPbBoundaryDetection.

Method Summary

Modifier and Type	Method	Description
private void	assignTextons(int[][] map, double[][][][] fim, double[][] textons)
private void	cgmo(double[][][][] cg, double[] theta, ModelImage image, double[] radius, int numOrientations, int nbins, double sigmaSim, double gamma, String smooth, double[] sigmaSmooth)	cgmo for color Compute the color gradient at a single scale and multiple orientations
private void	cgmo(double[][][][] cg, double[] theta, ModelImage image, double[] radius, int numOrientations, String smooth, double[] sigmaSmooth)
private void	cgmo(double[][][] cg, double[] theta, ModelImage image, double radius, int numOrientations, int nbins, double sigmaSim, String smooth, double sigmaSmooth)	cgmo for black and white Compute the color gradient at a single scale and multiple orientations
private void	cgmo(double[][][] cg, double[] theta, ModelImage image, double radius, int numOrientations, String smooth, double sigmaSmooth)
private void	conv2(double[][] A, double[][] B, double[][] Cout)
private void	det2MM(double[][] e0, double[][] e1, double[][] theta, double sigmaI, double sigmaO)
private void	detBG(double[][][] bg, double[] theta)
private void	detBGTG(double[][][] bg, double[][][] tg, double[] theta)
private void	detCG(double[][][][] cg, double[] theta)
private void	detCGTG(double[][][][] cg, double[][][] tg, double[] theta)
private void	detGM(double[][] m, double[][] theta, double sigma)
private void	detTG(double[][][] tg, double[] theta)
private void	distsqr(double[][] z, double[][] x, double[][] y)
private void	fbRun(double[][][][] fim, double[][][][] fb, double[][] im)
private void	fbRun(double[][] fim, double[][] fb, double[][] im)
private void	fftconv2(double[][] fim, double[][] im, double[][] f)
private void	fitparab(double[][] a, double[][] b, double[][] c, double[][] z, double ra, double rb, double theta)
final int	getInt(boolean bigEndian)	Reads four signed bytes from file.
final long	getLong(boolean bigEndian)	Reads eight unsigned bytes from file.
final String	getString(int length)	Reads a string from a file of given length.
final int	getUnsignedShort(boolean bigEndian)	Reads two unsigned bytes from file.
private void	nonmax(double[][] imout, double[][] im, double theta)
private void	nonmax(double[][] imout, double[][] im, double[][] theta)
private void	oeFilter(double[][] f, double sigmaX, double sigmaY, int support)
private void	oeFilter(double[][] f, double sigmaX, double sigmaY, int support, double theta)
private void	oeFilter(double[][] f, double sigmaX, double sigmaY, int support, double theta, int deriv)
private void	oeFilter(double[][] f, double sigmaX, double sigmaY, int support, double theta, int deriv, boolean dohil, boolean dovis)	Compute unit L1- norm 2D filter.
private void	padReflect(double[][] impad, double[][] im, int r)
private void	pb2MM(double[][] pb, double[][] theta)
private void	pb2MM2(double[][] pb, double[][] theta)
private void	pbBG(double[][] pb, double[][] theta)
private void	pbBGTG(double[][] pb, double[][] theta)
private void	pbCanny(double[][] pb)
private void	pbCG(double[][] pb, double[][] theta)
private void	pbCGTG(double[][] pb, double[][] theta)
private void	pbGM(double[][] pb, double[][] theta)
private void	pbGM2(double[][] pb, double[][] theta)
private void	pbTG(double[][] pb, double[][] theta)
private String	readCString()
private void	readFile(double[][][][] fb, double[][] tex, double[][] tsim)
private void	RGB2Lab(double[][][] L, double[] red, double[] green, double[] blue)
void	runAlgorithm()	Actually runs the algorithm.
private void	savgol(double[][] c, double[][] z, int d, int k, double ra, double rb, double theta)
private void	tgmo(double[][][] tg, double[] theta, int[][] tmap, int ntex, double radius, int numOrientations, double[][] tsim, String smooth, double sigma)	Compute the texture gradient at a single scale and multiple orientations
private void	tgso(double[][] tg, int[][] tmap, int ntex, double radius, double theta, String smooth, double sigma, double[][] tsim)	Compute the texture graident at a single orientation and scale

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

BGTG

private static final int BGTG

See Also:

• Constant Field Values

CGTG

private static final int CGTG

See Also:

• Constant Field Values

BG

private static final int BG

See Also:

• Constant Field Values

CG

private static final int CG

See Also:

• Constant Field Values

TG

private static final int TG

See Also:

• Constant Field Values

GM

private static final int GM

See Also:

• Constant Field Values

GM2

private static final int GM2

See Also:

• Constant Field Values

TWOMM

private static final int TWOMM

See Also:

• Constant Field Values

TWOMM2

private static final int TWOMM2

See Also:

• Constant Field Values

CANNY

private static final int CANNY

See Also:

• Constant Field Values

gradientType

private int gradientType

GRAY_PRESENTATION

private static final int GRAY_PRESENTATION

See Also:

• Constant Field Values

COLOR_PRESENTATION

private static final int COLOR_PRESENTATION

See Also:

• Constant Field Values

presentation

private int presentation

lowRadius

private double lowRadius

highRadius

private double highRadius

numOrientations

private int numOrientations

smooth

private String smooth

sigma

private double sigma

nthresh

private int nthresh

hmult

private double hmult

xDim

private int xDim

yDim

private int yDim

raFile

private RandomAccessFile raFile

byteShortBuffer

private final byte[] byteShortBuffer

byte array for short *

byteIntBuffer

private final byte[] byteIntBuffer

byte array for int *

byteLongBuffer

private final byte[] byteLongBuffer

byte array for long *

epsilon

private final double epsilon

Constructor Details

AlgorithmPbBoundaryDetection

public AlgorithmPbBoundaryDetection()

AlgorithmPbBoundaryDetection - default constructor.

AlgorithmPbBoundaryDetection

public AlgorithmPbBoundaryDetection(ModelImage destImg,
 ModelImage srcImg,
 int gradientType,
 int presentation,
 double lowRadius,
 double highRadius,
 int numOrientations,
 String smooth,
 double sigma,
 int nthresh,
 double hmult)

AlgorithmPbBoundaryDetection.

Parameters:

destImg - DOCUMENT ME!

srcImg - DOCUMENT ME!

gradientType -

presentation -

lowRadius -

highRadius -

numOrientations -

smooth -

sigma -

Method Details

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

pbCanny

private void pbCanny(double[][] pb)

pb2MM2

private void pb2MM2(double[][] pb,
 double[][] theta)

pb2MM

private void pb2MM(double[][] pb,
 double[][] theta)

pbCG

private void pbCG(double[][] pb,
 double[][] theta)

pbCGTG

private void pbCGTG(double[][] pb,
 double[][] theta)

pbGM2

private void pbGM2(double[][] pb,
 double[][] theta)

pbGM

private void pbGM(double[][] pb,
 double[][] theta)

pbBG

private void pbBG(double[][] pb,
 double[][] theta)

pbBGTG

private void pbBGTG(double[][] pb,
 double[][] theta)

pbTG

private void pbTG(double[][] pb,
 double[][] theta)

nonmax

private void nonmax(double[][] imout,
 double[][] im,
 double[][] theta)

nonmax

private void nonmax(double[][] imout,
 double[][] im,
 double theta)

det2MM

private void det2MM(double[][] e0,
 double[][] e1,
 double[][] theta,
 double sigmaI,
 double sigmaO)

Parameters:

e0 - output smaller eigenvlaues

e1 - output larger eigenvalues

theta - output Orientation of first eigenvector + PI/2 (i.e. orientation of possible edge)

sigmaI - input Inner scale (sigma for image derivatives)

sigmaO - input Outer scale (sigma for spatial averaging)

detCG

private void detCG(double[][][][] cg,
 double[] theta)

detCGTG

private void detCGTG(double[][][][] cg,
 double[][][] tg,
 double[] theta)

detGM

private void detGM(double[][] m,
 double[][] theta,
 double sigma)

detBG

private void detBG(double[][][] bg,
 double[] theta)

detBGTG

private void detBGTG(double[][][] bg,
 double[][][] tg,
 double[] theta)

detTG

private void detTG(double[][][] tg,
 double[] theta)

assignTextons

private void assignTextons(int[][] map,
 double[][][][] fim,
 double[][] textons)

distsqr

private void distsqr(double[][] z,
 double[][] x,
 double[][] y)

readFile

private void readFile(double[][][][] fb,
 double[][] tex,
 double[][] tsim)

getString

public final String getString(int length)
                       throws IOException

Reads a string from a file of given length.

Parameters:

length - Number of bytes that form the string.

Returns:

The string read from the file.

Throws:

IOException - if there is an error reading the file

getLong

public final long getLong(boolean bigEndian)
                   throws IOException

Reads eight unsigned bytes from file.

Parameters:

bigEndian - true indicates big endian byte order, false indicates little endian.

Returns:

The value of the long read from the file.

Throws:

IOException - if there is an error reading the file

getInt

public final int getInt(boolean bigEndian)
                 throws IOException

Reads four signed bytes from file.

Parameters:

bigEndian - true indicates big endian byte order, false indicates little endian.

Returns:

The value of the integer read from the file.

Throws:

IOException - if there is an error reading the file

getUnsignedShort

public final int getUnsignedShort(boolean bigEndian)
                           throws IOException

Reads two unsigned bytes from file.

Parameters:

bigEndian - true indicates big endian byte order, false indicates little endian.

Returns:

The value of unsigned short read from the file returned as an int.

Throws:

IOException - if there is an error reading the file

readCString

private String readCString()
                    throws IOException

Throws:

IOException

cgmo

private void cgmo(double[][][][] cg,
 double[] theta,
 ModelImage image,
 double[] radius,
 int numOrientations,
 String smooth,
 double[] sigmaSmooth)

cgmo

private void cgmo(double[][][][] cg,
 double[] theta,
 ModelImage image,
 double[] radius,
 int numOrientations,
 int nbins,
 double sigmaSim,
 double gamma,
 String smooth,
 double[] sigmaSmooth)

cgmo for color Compute the color gradient at a single scale and multiple orientations

Parameters:

cg - output output [yDim][xDim][3][numOrientations] array for color

image - RGB image, values in [0, 1].

radius - Radius of disc for cg array

numOrientations - Number of orientations for cg array

nbins - Number of bins; should be > 1/sigmaSim.

sigmaSim - For color similarity function

gamma - Gamma correction for LAB [2.5].

smooth - Smoothing method, one of {"gaussian", "savgol", "none"}, default none

sigmaSmooth - Sigma for smoothing, default to radius

output - [numOrientations] theta

RGB2Lab

private void RGB2Lab(double[][][] L,
 double[] red,
 double[] green,
 double[] blue)

cgmo

private void cgmo(double[][][] cg,
 double[] theta,
 ModelImage image,
 double radius,
 int numOrientations,
 String smooth,
 double sigmaSmooth)

cgmo

private void cgmo(double[][][] cg,
 double[] theta,
 ModelImage image,
 double radius,
 int numOrientations,
 int nbins,
 double sigmaSim,
 String smooth,
 double sigmaSmooth)

cgmo for black and white Compute the color gradient at a single scale and multiple orientations

Parameters:

cg - output [yDim][xDim][numOrientations] array for black and white

image - Grayscale image, values in [0, 1].

radius - Radius of disc for cg array

numOrientations - Number of orientations for cg array

nbins - Number of bins; should be > 1/sigmaSim.

sigmaSim - For color similarity function

smooth - Smoothing method, one of {"gaussian", "savgol", "none"}, default none

sigmaSmooth - Sigma for smoothing, default to radius

output - [numOrientations] theta

tgmo

private void tgmo(double[][][] tg,
 double[] theta,
 int[][] tmap,
 int ntex,
 double radius,
 int numOrientations,
 double[][] tsim,
 String smooth,
 double sigma)

Compute the texture gradient at a single scale and multiple orientations

Parameters:

tmap - [yDim][xDim] Texton map, values in [1, ntex]

ntex - Number of textons

radius - Radius of disc for texture gradient

numOrientations - Number of orientations at which to compute the texture graident

tsim - Texton similarity matrix. If not provided, then use chi-squared.

smooth - Smoothing method. One of "gaussian", "savgol", "none". Default "none".

sigma - Sigma for smoothing. Default to radius.

output - tg [yDim][xDim][numOrientations] array

output - [numOrientations] theta Disc orientations (which are orthogonal to the texture gradient).

tgso

private void tgso(double[][] tg,
 int[][] tmap,
 int ntex,
 double radius,
 double theta,
 String smooth,
 double sigma,
 double[][] tsim)

Compute the texture graident at a single orientation and scale

Parameters:

tmap - [yDim][xDim] Texton map, values in [1, ntex].

ntex - Number of textons

radius - Radius of disc for tg

theta - Orientation orthogonal to tg.

smooth - Smoothing method, one of {"gaussian", "savgol", "none"}, default = "none".

sigma - Sigma for smoothing. Default to radius.

tsim - [ntex][ntex] Texton similarity matrix. If not provided, then use chi-squared.

output - tg [yDim][xDim] array

fitparab

private void fitparab(double[][] a,
 double[][] b,
 double[][] c,
 double[][] z,
 double ra,
 double rb,
 double theta)

savgol

private void savgol(double[][] c,
 double[][] z,
 int d,
 int k,
 double ra,
 double rb,
 double theta)

fbRun

private void fbRun(double[][][][] fim,
 double[][][][] fb,
 double[][] im)

fbRun

private void fbRun(double[][] fim,
 double[][] fb,
 double[][] im)

fftconv2

private void fftconv2(double[][] fim,
 double[][] im,
 double[][] f)

padReflect

private void padReflect(double[][] impad,
 double[][] im,
 int r)

oeFilter

private void oeFilter(double[][] f,
 double sigmaX,
 double sigmaY,
 int support)

oeFilter

private void oeFilter(double[][] f,
 double sigmaX,
 double sigmaY,
 int support,
 double theta)

oeFilter

private void oeFilter(double[][] f,
 double sigmaX,
 double sigmaY,
 int support,
 double theta,
 int deriv)

oeFilter

private void oeFilter(double[][] f,
 double sigmaX,
 double sigmaY,
 int support,
 double theta,
 int deriv,
 boolean dohil,
 boolean dovis)

Compute unit L1- norm 2D filter. The filter is a Gaussian in the x direction The filter is a Gaussian derivative with optional Hilbert transform in the y direction. The filter is zero-meaned if deriv > 0.

Parameters:

f - output [sz][sz] square filter

sigmaX -

sigmaY -

support - Make filter +/- this many sigma

theta - Orientation of x axis, in radians

deriv - Degree of y derivative, one of {0, 1, 2}.

dohil - Do Hilbert transform in y direction?

dovis - Visualization for debugging?

conv2

private void conv2(double[][] A,
 double[][] B,
 double[][] Cout)